rs11693697

Variant names:

• chr2-102299202-T-C
• rs11693697
• ENST00000804381.1:n.698+584T>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000804381.1(ENSG00000304533):​n.698+584T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.126 in 152,186 control chromosomes in the GnomAD database, including 1,646 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.13 (1646 hom., cov: 32)
• Consequence: ENSG00000304533 ENST00000804381.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.258
• Publications: 17 publications found

Genes affected

ENSG00000304533 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.184 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000804381.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000304533	ENST00000804381.1		n.698+584T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.126 AC: 19233 AN: 152068 Hom.: 1646 Cov.: 32

Gnomad AFR AF: 0.0338

Gnomad AMI AF: 0.211

Gnomad AMR AF: 0.116

Gnomad ASJ AF: 0.126

Gnomad EAS AF: 0.00192

Gnomad SAS AF: 0.0680

Gnomad FIN AF: 0.200

Gnomad MID AF: 0.0886

Gnomad NFE AF: 0.187

Gnomad OTH AF: 0.133

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.126 AC: 19225 AN: 152186 Hom.: 1646 Cov.: 32 AF XY: 0.125 AC XY: 9291 AN XY: 74402

African (AFR) AF: 0.0337 AC: 1400 AN: 41560

American (AMR) AF: 0.115 AC: 1766 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.126 AC: 438 AN: 3472

East Asian (EAS) AF: 0.00193 AC: 10 AN: 5188

South Asian (SAS) AF: 0.0674 AC: 325 AN: 4820

European-Finnish (FIN) AF: 0.200 AC: 2111 AN: 10574

Middle Eastern (MID) AF: 0.0850 AC: 25 AN: 294

European-Non Finnish (NFE) AF: 0.187 AC: 12679 AN: 67960

Other (OTH) AF: 0.132 AC: 279 AN: 2112

Alfa AF: 0.158 Hom.: 4401

Bravo AF: 0.117

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.16
DANN	Benign	0.45
PhyloP100		-0.26

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs11693697; hg19: chr2-102915662;